Microbial gene profiles based on RNA and DNA reveal variation in functional resources across urban soils.

Background/Question/Methods

Soils in human-dominated landscapes face multiple anthropogenic stresses driven by urbanization. This complicates sustainability efforts since soil bacteria, archaea, and fungi contain the metabolic machinery to process the majority of nutrient and energy transformations in terrestrial ecosystems, providing key ecosystem services. Although recent efforts have begun to characterize variation in urban microbial community composition, we still know little about how urban environments shape the diversity and function of the microbial genetic resources that underlie specific ecological functions. We investigated two questions to address this gap: (1) Does urban land management create microhabitats that structure the availability and expression of functional genetic resources? (2) How does the expression of functional genes based on RNA differ from their potential availability based on DNA? We profiled 16s rRNA and functional gene diversity from two engineered soil types (enhanced tree pits and streetside bioswales designed to absorb stormwater runoff) and two non-engineered soils (standard tree pits and city parks), in the Bronx, NY. Gene profiles are based on Illumina sequencing of PCR amplicons—using both RNA and DNA templates—focusing on eight genes related to C cycling (CO₂assimilation, methane degradation, contaminant degradation), N cycling (denitrification, nitrification) and S cycling. 

Results/Conclusions

We found that urban soil microhabitats are associated with distinct microbial communites. Each of the four soil types had distinct community diversity based on 16s OTU clustering, and engineered soils were differentiated from non-engineered soils. Urban soils also differed in the potential and expressed diversity of functional genes, though the precise patterns varied by gene. Estimates of both community composition and functional gene diversity were significantally different when based on RNA than when based on DNA. These results indicates that microbial community composition may often be a poor proxy for assessing the diversity of functional genes that underlie ecosystem services. They also highlight the importance of examining RNA, since expressed genetic profiles can be quite distinct from genomic DNA profiles. This work demonstrates a potential method for microbial bio-monitoring that could help quantify how urban land management practices impact soil metagenomic resources.